how to bake texture from multiple overlayed uv Islands to individual uv islands
Create a second UV map on your object in Properties &gt; Object Data and unwrap it so it has individual islands (or however you want)



Blender Internal

Add your existing texture to the object and select the appropriate UV map in Properties &gt; Textures &gt; Mapping &gt; Map:


Create a new image in the UV/Image editor by pressing AltN or Header &gt; Image &gt; New

Select the new UV map in Properties &gt; Object Data and then select the new image in the image editor, so that the individual islands UV map is displayed over the new image.


Press Bake in Properties &gt; Render &gt; Bake:



Cycles
To do the same in cycles, you can use attribute nodes:

Add two attribute nodes and enter the names of your UV maps. You can now use the Vector output of these as those UV coordinates.

Create a new image in the image editor and add it to the node setup with a texture node. Plug the mapping you want into that texture node and select it.


With that texture node selected, press Bake in Render settings &gt; Bake.